Related papers: Molecular dynamics simulation of multivalent ion m…
The dynamics of hydrogen bonds among water molecules themselves and with the polar head groups (PHG) at a micellar surface have been investigated by long molecular dynamics simulations. The lifetime of the hydrogen bond between a PHG and a…
A model system of highly asymmetric polyelectrolyte with directional short-range attractive interactions was studied by canonical Monte Carlo computer simulations. Comparison of MC data with previously published theoretical results shows…
We have studied the general aspects of the dynamics of an ion trapped in an ideal multipolar radiofrequency trap while interacting with a dense cold atomic gas. In particular, we have explored the dynamical stability, the energy relaxation…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…
The genome contains genetic information essential for cell's life. The genome's spatial organization inside the cell nucleus is critical for its proper function including gene regulation. The two major genomic compartments -- euchromatin…
Structuring of DNA counterions around the double helix has been studied by the molecular dynamics method. A DNA dodecamer d(CGCGAATTCGCG) in water solution with the alkali metal counterions Na$^{+}$, K$^{+}$, and Cs$^{+}$ has been…
In human cells, estrogenic signals induce cyclical association and dissociation of specific proteins with the DNA in order to activate transcription of estrogen-responsive genes. These oscillations can be modeled by assuming a large number…
Explicit molecular dynamics simulations were applied to a pair of amorphous silica nanoparticles of diameter 3.2 nm immersed in a background electrolyte. Mean forces acting between the pair of silica nanoparticles were extracted at four…
A discrete multistate kinetic model for water-wire proton transport is constructed and analyzed using Monte-Carlo simulations. The model allows for each water molecule to be in one of three states: oxygen lone pairs pointing leftward,…
Using Brownian dynamics simulations, we systematically study the effective interaction between two parallel hard walls in a 2D suspension of self-propelled (active) colloidal hard spheres, and we find that the effective force between two…
The filtration of fluid in 2D porous medium is simulated by the molecular dynamics technique. The high concentration of fluid is created at the initial point in time and the number of fluid particles is investigated in all porous. The…
Specific molecular interactions underlie unexpected and useful phenomena in nanofluidic systems, but require descriptions that go beyond traditional macroscopic hydrodynamics. In this letter, we demonstrate how equilibrium molecular…
Basic problems of the semiclassical microscopic modelling of strongly interactingsystems are discussed within the framework of Quantum Molecular Dynamics (QMD). This model allows to study the influence of several types of nucleonic…
We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…
New Molecular Dynamics simulations have been carried out in order to get an insight on the physical mechanisms that determine the drift mobility of negative Oxygen ions in very dense Neon gas in the supercritical phase close to the critical…
The adhesive contact between elastic solids with randomly rough, self affine fractal surfaces is studied by molecular dynamics (MD) simulations. The interfacial binding energy obtained from the simulations of nominally flat and curved…
Strong influence of water molecules on the transport and magnetic properties of DNA, observed in this study, opens up real opportunities for application of DNA in molecular electronics. Interaction of the nucleobases with water molecules…
Emergent bath-mediated attraction and condensation arise when multiple particles are simultaneously driven through an equilibrated bath under geometric constraints. While such scenarios are observed in a variety of non-equilibrium…
We report a new Quantum Mechanical/Molecular Dynamics (QM/MD) simulation loop to model the coupling between the electron and atom dynamics in solid/liquid interfacial systems. The method can describe simultaneously both the quantum…